Query         gi|254780854|ref|YP_003065267.1| NADH dehydrogenase subunit C [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 202
No_of_seqs    224 out of 1237
Neff          5.9 
Searched_HMMs 39220
Date          Sun May 29 23:41:10 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780854.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PRK06074 NADH dehydrogenase su 100.0       0       0  510.6  17.5  188    2-199     1-189 (190)
  2 KOG1713 consensus              100.0       0       0  454.6   4.4  187    3-189     2-189 (191)
  3 PRK07785 NADH dehydrogenase su 100.0       0       0  417.2  14.1  156    6-162    67-227 (238)
  4 COG0852 NuoC NADH:ubiquinone o 100.0       0       0  405.7  11.6  174    1-177     1-176 (176)
  5 TIGR01961 NuoC_fam NADH (or F4 100.0       0       0  398.2   8.9  123   30-152     1-136 (136)
  6 PRK08491 NADH dehydrogenase su 100.0       0       0  388.1   9.3  132   19-153    48-179 (263)
  7 PRK11742 bifunctional NADH:ubi 100.0       0       0  344.4  11.2  143    9-152     2-153 (575)
  8 PRK13292 trifunctional NADH de 100.0       0       0  310.7  10.6  147    7-153   219-371 (784)
  9 CHL00012 ndhJ NADH dehydrogena 100.0 5.6E-45       0  295.3  11.5  126   28-157    25-155 (158)
 10 PRK12494 NADH dehydrogenase su 100.0 1.8E-42       0  279.7  10.3  124   30-157    41-169 (172)
 11 PRK07735 NADH dehydrogenase su 100.0 2.8E-41 1.4E-45  272.4   7.0  141    5-148   268-413 (420)
 12 pfam00329 Complex1_30kDa Respi 100.0 6.9E-38 1.8E-42  251.8   8.3  102   41-146     1-103 (103)
 13 COG3262 HycE Ni,Fe-hydrogenase  99.9 1.8E-27 4.6E-32  188.4   9.4  144    1-148     1-151 (165)
 14 PRK02224 chromosome segregatio  42.9      30 0.00076   16.5   3.9   18  106-123   108-125 (880)
 15 PRK06452 sdhA succinate dehydr  41.0      25 0.00064   17.0   2.6   18   53-70    150-167 (566)
 16 TIGR00538 hemN oxygen-independ  40.8      32 0.00082   16.3   4.3   53    3-65    121-175 (462)
 17 PRK05253 sulfate adenylyltrans  38.9      13 0.00032   18.8   0.8  111   35-156   111-258 (300)
 18 pfam00828 Ribosomal_L18e Ribos  37.1     9.8 0.00025   19.4   0.1   34  138-175    24-59  (122)
 19 TIGR02166 dmsA_ynfE anaerobic   36.2      14 0.00035   18.5   0.7   69   75-151   642-724 (849)
 20 KOG1372 consensus               35.6      15 0.00039   18.3   0.8   20  113-133   198-220 (376)
 21 pfam01305 consensus             32.9      14 0.00035   18.5   0.2   33  137-175    48-82  (102)
 22 pfam10364 NKWYS Putative capsu  31.9      12  0.0003   19.0  -0.3   25  106-130    31-55  (141)
 23 PRK12563 sulfate adenylyltrans  31.9      16 0.00041   18.1   0.5  113   38-159   125-273 (312)
 24 COG1334 FlaG Uncharacterized f  30.7      47  0.0012   15.3   3.3   39   16-54     77-116 (120)
 25 TIGR01472 gmd GDP-mannose 4,6-  28.7      26 0.00065   16.9   1.1  107    7-132    71-196 (365)
 26 PRK05592 rplO 50S ribosomal pr  28.3      18 0.00046   17.8   0.2   38  136-180    47-86  (144)
 27 pfam09860 DUF2087 Uncharacteri  26.3     3.3 8.5E-05   22.3  -3.8   35  105-139    24-58  (71)
 28 TIGR02374 nitri_red_nirB nitri  23.5      11 0.00028   19.1  -1.6   31  117-147   615-646 (813)
 29 pfam09234 DUF1963 Domain of un  23.2      64  0.0016   14.5   3.7   15   65-79     62-76  (221)
 30 PRK04290 30S ribosomal protein  21.1      62  0.0016   14.5   1.8   20  137-156    56-75  (115)
 31 pfam02485 Branch Core-2/I-Bran  20.6      72  0.0018   14.2   2.5   28   40-69     77-104 (242)
 32 pfam06283 ThuA Trehalose utili  20.2      34 0.00087   16.1   0.3  106   42-152    22-134 (216)
 33 COG2125 RPS6A Ribosomal protei  20.2      66  0.0017   14.4   1.8   19  138-156    58-76  (120)
 34 KOG0105 consensus               20.0      43  0.0011   15.5   0.8   30  102-131   120-164 (241)

No 1  
>PRK06074 NADH dehydrogenase subunit C; Provisional
Probab=100.00  E-value=0  Score=510.60  Aligned_cols=188  Identities=52%  Similarity=0.990  Sum_probs=182.8

Q ss_pred             CHHHHHHHHHHHHHCCCCEEEEEEECCCEEEEECHHHHHHHHHHHHHCCCCCCCEEEECCCCCCCCCCCCEEEEEEEEEC
Q ss_conf             05799999999986153114579847959999868989999999871878980147513256887777857999996615
Q gi|254780854|r    2 VRKIEDLGDYIVNSFSGSVRFAVNSVGELSLDVDCGDLVSLCSFLRDDPHCCFVNIIDLCGVDFLSRSNRFDVVYHFLSP   81 (202)
Q Consensus         2 ~~~L~~L~~~L~~~l~~~I~~~~~~~~el~i~V~~~~l~~vl~~LKdd~~~~F~~LiDItaVDyp~~~~RFeVvY~LlS~   81 (202)
                      +++|++|++.|+++||++|..+...+|+++|.|+++++.++|++||++++|+|++|+||||||||++++||+|||||+|+
T Consensus         1 ~e~l~eL~~~L~~~f~~~I~~~~~~~gelti~V~~~~l~evl~~LKdd~~~~Fd~L~DltaVDy~~~~~RFeVVYhL~S~   80 (190)
T PRK06074          1 SEKLEELIAYLEAKLPDAIVSVTVAFGELTLEVPAEKILEVLKFLRDDPELRFEQLIDLTGVDYPGREKRFEVVYHLLSV   80 (190)
T ss_pred             CHHHHHHHHHHHHHHCHHHHEEEEECCCEEEEECHHHHHHHHHHHHCCCCCCCCEEEEEEEECCCCCCCEEEEEEEEEEC
T ss_conf             96699999999987241211278889927999819999999999855988998705245847268988879999998785


Q ss_pred             CCCCEEEEEEEECCC-CEEECCCCCEECCCCEECCCHHHCCCEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECH
Q ss_conf             752059982120578-5010122330255310112101138273567987677889989878711337789844788762
Q gi|254780854|r   82 KYNRRLRVKIAVAEG-KSVPSIVGIYPGADWFEREVWDMYGIFFEGHPDLRRILTDYGFEGHPLRKDFPVTGFVELHYDD  160 (202)
Q Consensus        82 ~~n~ri~Vk~~v~e~-~~vpSi~~i~p~A~W~ERE~~DmfGI~F~gHPdlRRiL~d~~feGhPLRKDFPltG~~evryd~  160 (202)
                      ++|+||+||+.++++ +.||||++|||||||+|||+||||||.|+|||||||||+|++|+||||||||||+||+|||||+
T Consensus        81 ~~~~ri~vk~~~~~~~p~ipSit~iw~~AnW~ERE~yDmfGI~F~gHPdLrRill~~~~~GhPLRKDyPl~g~~~~~y~~  160 (190)
T PRK06074         81 KHNQRLRVKVRAPEDFPVVPSVVDIWPSANWYEREAYDLYGIVFEGHPDLRRILTDYGFEGHPLRKDFPLTGYVEVRYDE  160 (190)
T ss_pred             CCCCEEEEEECCCCCCCCCCCCHHEEECCCEEEEEHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECH
T ss_conf             68988999953677899798432123179745555245409423799986131589898778716774688731451074


Q ss_pred             HHCEEECCCCEEEEHHHCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             115131266422022212766563234533457533210
Q gi|254780854|r  161 KVKKVVYRPVELMQEHRDYDFLSPWEGVNSLFAKEDSKD  199 (202)
Q Consensus       161 ~~k~v~~epv~l~q~~r~f~~~spwe~~~~~~~~~~~~~  199 (202)
                      ++|||+|+||+|          |||+|..+++++|+|+.
T Consensus       161 ~~~~v~~~~~~~----------~~~~~~~~v~~~~~~~~  189 (190)
T PRK06074        161 ELKRVVYEPVTL----------SPWEGTPYVLPGDEKAG  189 (190)
T ss_pred             HHCEEEECCCCC----------CCCCCCCCCCCCCCCCC
T ss_conf             347585126645----------73258884676866678


No 2  
>KOG1713 consensus
Probab=100.00  E-value=0  Score=454.64  Aligned_cols=187  Identities=45%  Similarity=0.861  Sum_probs=178.2

Q ss_pred             HHHHHHHHHHHHHCCCCEEEEEEE-CCCEEEEECHHHHHHHHHHHHHCCCCCCCEEEECCCCCCCCCCCCEEEEEEEEEC
Q ss_conf             579999999998615311457984-7959999868989999999871878980147513256887777857999996615
Q gi|254780854|r    3 RKIEDLGDYIVNSFSGSVRFAVNS-VGELSLDVDCGDLVSLCSFLRDDPHCCFVNIIDLCGVDFLSRSNRFDVVYHFLSP   81 (202)
Q Consensus         3 ~~L~~L~~~L~~~l~~~I~~~~~~-~~el~i~V~~~~l~~vl~~LKdd~~~~F~~LiDItaVDyp~~~~RFeVvY~LlS~   81 (202)
                      .++..++++..+.+++.++..... .+++.+.+.++.++.|+.|||++..++|..++||||||-|.+++||+|||+|+|.
T Consensus         2 ~q~~~fg~ya~e~Lpk~~~k~~~~~~~~lei~~~~~~~i~vl~flk~h~y~r~q~~~Diagvdvp~rk~rfevvynl~sv   81 (191)
T KOG1713           2 MQLTLFGKYAAECLPKRVQKVQYQAGDELEILIHPDGVIPVLLFLKGHTYARFQNLYDIAGVDVPTRKNRFEVVYNLLSV   81 (191)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEECCCCCEEEEEEEEECCCCEEEEEEEEECCCCCCCCCCEEEEEEEECCC
T ss_conf             40558899998751388776443035420430477864677766616450146676764377865634436775300101


Q ss_pred             CCCCEEEEEEEECCCCEEECCCCCEECCCCEECCCHHHCCCEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECHH
Q ss_conf             75205998212057850101223302553101121011382735679876778899898787113377898447887621
Q gi|254780854|r   82 KYNRRLRVKIAVAEGKSVPSIVGIYPGADWFEREVWDMYGIFFEGHPDLRRILTDYGFEGHPLRKDFPVTGFVELHYDDK  161 (202)
Q Consensus        82 ~~n~ri~Vk~~v~e~~~vpSi~~i~p~A~W~ERE~~DmfGI~F~gHPdlRRiL~d~~feGhPLRKDFPltG~~evryd~~  161 (202)
                      ..|.||||||+++|.+||+|++++|+||||+|||+||||||.|.|||||||||||||||||||||||||+||+|||||++
T Consensus        82 r~nsrirVkt~tde~tpI~sv~~vfksad~~EREv~DM~GV~f~nHPdLrRIltdygfeGhPlRKDyplsgy~Evryd~~  161 (191)
T KOG1713          82 RYNSRIRVKTYTDESTPIDSVVSVFKSADWQEREVWDMFGVTFDNHPDLRRILTDYGFEGHPLRKDYPLSGYVEVRYDDE  161 (191)
T ss_pred             CCCCEEEEEEECCCCCCCCCCEEEEECCCHHHHHHHHHHCEECCCCCCHHHHCCCCCCCCCCCCCCCCCCCCEEEECCCH
T ss_conf             23546899983156766775057541587478778766423104786532204666645785224677888268750652


Q ss_pred             HCEEECCCCEEEEHHHCCCCCCCCCCCC
Q ss_conf             1513126642202221276656323453
Q gi|254780854|r  162 VKKVVYRPVELMQEHRDYDFLSPWEGVN  189 (202)
Q Consensus       162 ~k~v~~epv~l~q~~r~f~~~spwe~~~  189 (202)
                      +||||+||++|+||||.||+.||||...
T Consensus       162 ~krvv~ep~elaqefr~fd~~spwe~~~  189 (191)
T KOG1713         162 EKRVVSEPIELAQEFRKFDLNSPWEQFP  189 (191)
T ss_pred             HCEEECCHHHHHHHHHHCCCCCCHHHCC
T ss_conf             3023327689999876453589356467


No 3  
>PRK07785 NADH dehydrogenase subunit C; Provisional
Probab=100.00  E-value=0  Score=417.21  Aligned_cols=156  Identities=35%  Similarity=0.695  Sum_probs=144.8

Q ss_pred             HHHHHHHHH---HCCCCEEEEEEECCCEEEEECHHHHHHHHHHHHHCCCCCCCEEEECCCCCCCCCC-CCEEEEEEEEEC
Q ss_conf             999999998---6153114579847959999868989999999871878980147513256887777-857999996615
Q gi|254780854|r    6 EDLGDYIVN---SFSGSVRFAVNSVGELSLDVDCGDLVSLCSFLRDDPHCCFVNIIDLCGVDFLSRS-NRFDVVYHFLSP   81 (202)
Q Consensus         6 ~~L~~~L~~---~l~~~I~~~~~~~~el~i~V~~~~l~~vl~~LKdd~~~~F~~LiDItaVDyp~~~-~RFeVvY~LlS~   81 (202)
                      ++|...+.+   .++++|+++.+.+||+++.|.+++|.+|+++||||++|+|++|+||||||||++. .||+|||||+|+
T Consensus        67 d~L~~a~~~~~~~~~~aie~vvVdrgELTl~V~re~l~~V~~~LRDdp~lrFe~l~dvtGVDYP~~~~rrf~vVYhLlS~  146 (238)
T PRK07785         67 DRLAEALEEEGVEFGDAIEKVVVDRGELTLHVRRERLPEVAQTLRDDPALRFELCLGVSGVHYPDDTGRELHAVYPLTSI  146 (238)
T ss_pred             HHHHHHHHHCCCCHHHHEEEEEEECCEEEEEECHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEECCC
T ss_conf             99999987705565442137888688389998789999999987079655562021544545687567643699982378


Q ss_pred             CCCCEEEEEEEECCCCE-EECCCCCEECCCCEECCCHHHCCCEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECH
Q ss_conf             75205998212057850-10122330255310112101138273567987677889989878711337789844788762
Q gi|254780854|r   82 KYNRRLRVKIAVAEGKS-VPSIVGIYPGADWFEREVWDMYGIFFEGHPDLRRILTDYGFEGHPLRKDFPVTGFVELHYDD  160 (202)
Q Consensus        82 ~~n~ri~Vk~~v~e~~~-vpSi~~i~p~A~W~ERE~~DmfGI~F~gHPdlRRiL~d~~feGhPLRKDFPltG~~evryd~  160 (202)
                      ++|.|||||+.+++..+ ||||++|||+|||+|||+||||||.|+||||||||||||+|+||||||||||+| ++|+|..
T Consensus       147 ~~N~RiRlkv~v~e~dP~vpSv~~v~~~AnW~ERE~~DmfGI~F~GHPdLrRIlmp~d~~GHPlRKD~PL~G-ipVeYkg  225 (238)
T PRK07785        147 THNRRIRLEVAAPDSDPHIPSLVSVYPTNDWHERETYDFFGIIFDGHPALTRIEMPDDWQGHPQRKDYPLGG-IPVEYKG  225 (238)
T ss_pred             CCCCEEEEEEECCCCCCCCCCCCCCCCCCCHHHHHHHHHCCEEECCCCCCCCCCCCCCCCCCCCCCCCCCCC-CEEEECC
T ss_conf             779889999975888985885323356887467645400052247999861036899998775356767887-2574168


Q ss_pred             HH
Q ss_conf             11
Q gi|254780854|r  161 KV  162 (202)
Q Consensus       161 ~~  162 (202)
                      .+
T Consensus       226 a~  227 (238)
T PRK07785        226 AQ  227 (238)
T ss_pred             CC
T ss_conf             86


No 4  
>COG0852 NuoC NADH:ubiquinone oxidoreductase 27 kD subunit [Energy production and conversion]
Probab=100.00  E-value=0  Score=405.65  Aligned_cols=174  Identities=48%  Similarity=0.879  Sum_probs=162.4

Q ss_pred             CCHH-HHHHHHHHHHHCCCCEEEEEEECCCEEEEECHHHHHHHHHHHHHCCCCCCCEEEECCCCCCCCCCCCEEEEEEEE
Q ss_conf             9057-999999999861531145798479599998689899999998718789801475132568877778579999966
Q gi|254780854|r    1 MVRK-IEDLGDYIVNSFSGSVRFAVNSVGELSLDVDCGDLVSLCSFLRDDPHCCFVNIIDLCGVDFLSRSNRFDVVYHFL   79 (202)
Q Consensus         1 M~~~-L~~L~~~L~~~l~~~I~~~~~~~~el~i~V~~~~l~~vl~~LKdd~~~~F~~LiDItaVDyp~~~~RFeVvY~Ll   79 (202)
                      |... +.++.+.+.+.++..+.......+++++.+.+..+.++|++||++.   |.+|+|+||||||++.+||+|||||+
T Consensus         1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~l~~Lk~~~---f~~l~d~~gvD~~~~~~~FevvYhL~   77 (176)
T COG0852           1 PDDPVLAELLERLLAELSTVIETVVVAEGELTLKVPPDELIDVLKALKDEG---FDHLLDLTGVDYPQETERFEVVYHLL   77 (176)
T ss_pred             CCCHHHHHHHHHHHHHHHHEEEEEEEEEEEEEEECCHHHHHHHHHHHHHHH---HHHHHHHHCCCCCCCCCCEEEEEEEE
T ss_conf             961356787776666320004210010016787347889999999974420---78898764565425688579999964


Q ss_pred             ECCCCCEEEEEEEECCCCE-EECCCCCEECCCCEECCCHHHCCCEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEE
Q ss_conf             1575205998212057850-101223302553101121011382735679876778899898787113377898447887
Q gi|254780854|r   80 SPKYNRRLRVKIAVAEGKS-VPSIVGIYPGADWFEREVWDMYGIFFEGHPDLRRILTDYGFEGHPLRKDFPVTGFVELHY  158 (202)
Q Consensus        80 S~~~n~ri~Vk~~v~e~~~-vpSi~~i~p~A~W~ERE~~DmfGI~F~gHPdlRRiL~d~~feGhPLRKDFPltG~~evry  158 (202)
                      |++.|.||+|||.++++.+ |||+++|||+|||+|||+||||||.|+|||||||||||+||+||||||||||+||++++|
T Consensus        78 s~~~~~~v~vkv~~~~~~~~vpSv~~I~~~A~W~ERE~yDmfGI~FeGHP~LrRilm~~~~~GhPLRKDfpl~~~~~~~~  157 (176)
T COG0852          78 SYKDNRRVRVKVRLSEDDPHVPSVTDIWPAANWYEREAYDMFGIVFEGHPDLRRILMPDDWEGHPLRKDFPLRGYVEVRY  157 (176)
T ss_pred             ECCCCCEEEEEEECCCCCCCCCCHHHHCCCCCHHHHHHHEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEECC
T ss_conf             06889789999886898886871577313576266633223125875996621435788878997567768886388341


Q ss_pred             CHHHCEEECCCCEEEEHHH
Q ss_conf             6211513126642202221
Q gi|254780854|r  159 DDKVKKVVYRPVELMQEHR  177 (202)
Q Consensus       159 d~~~k~v~~epv~l~q~~r  177 (202)
                      |+++|+++|+|+.+.|++|
T Consensus       158 ~~~~~~~~~~~~~~~~~~~  176 (176)
T COG0852         158 DEEDKKVVYEPVELIFERR  176 (176)
T ss_pred             CHHHCCCCCCCCCCCCCCC
T ss_conf             2120534456400156689


No 5  
>TIGR01961 NuoC_fam NADH (or F420H2) dehydrogenase, subunit C; InterPro: IPR010218   This entry describes the C subunit of the NADH dehydrogenase complex I in bacteria, as well as many instances of the corresponding mitochondrial subunit (NADH dehydrogenase subunit 9) and of the F420H2 dehydrogenase in Methanosarcina. Complex I contains subunits designated A-N. This C subunit often occurs as a fusion protein with the D subunit. This entry excludes the NAD(P)H and plastoquinone-dependent form of chloroplasts and Synechocystis.; GO: 0016651 oxidoreductase activity acting on NADH or NADPH, 0006118 electron transport.
Probab=100.00  E-value=0  Score=398.18  Aligned_cols=123  Identities=50%  Similarity=0.987  Sum_probs=118.0

Q ss_pred             EEEEECHHHHHHHHHHHHHCCCCCCCEEEECCCCC-CCC-----CCCCEEEEEEEEECCCCC----EEEEEEEECCCCE-
Q ss_conf             99998689899999998718789801475132568-877-----778579999966157520----5998212057850-
Q gi|254780854|r   30 LSLDVDCGDLVSLCSFLRDDPHCCFVNIIDLCGVD-FLS-----RSNRFDVVYHFLSPKYNR----RLRVKIAVAEGKS-   98 (202)
Q Consensus        30 l~i~V~~~~l~~vl~~LKdd~~~~F~~LiDItaVD-yp~-----~~~RFeVvY~LlS~~~n~----ri~Vk~~v~e~~~-   98 (202)
                      ++|.+.++.+.++|++||+|+.|+|++|+|+|||| ||+     +++||||||||+|+++|+    ||+|||.++++++ 
T Consensus         1 ~~v~~~~~~~~~v~~~Lk~d~~l~F~~L~d~~GVD~yp~~~~~l~~~~fevvY~L~S~~~~~~~~~~~~~Kv~~~~~d~~   80 (136)
T TIGR01961         1 LVVEIKKEQLLEVLTFLKDDPALGFELLSDVSGVDEYPKKERELREKRFEVVYHLLSIKHNQKRKSRIRIKVRLSEDDPN   80 (136)
T ss_pred             CEEEECHHHHHHHHHHCCCCCCCCEEEEEEEEEECCCCCCCCCCCCCCCCEEEEEECCCCCCCCCCEEEEEEEECCCCCC
T ss_conf             91563465689998740022216801566655310012578888876630566652363411147258999873789898


Q ss_pred             -EECCCCCEECCCCEECCCHHHCCCEECCCCCCCCCCCCCCCCC-CCCCCCCCCCC
Q ss_conf             -1012233025531011210113827356798767788998987-87113377898
Q gi|254780854|r   99 -VPSIVGIYPGADWFEREVWDMYGIFFEGHPDLRRILTDYGFEG-HPLRKDFPVTG  152 (202)
Q Consensus        99 -vpSi~~i~p~A~W~ERE~~DmfGI~F~gHPdlRRiL~d~~feG-hPLRKDFPltG  152 (202)
                       |||+++||+||||+|||+||||||.|+||||||||||||||+| |||||||||+|
T Consensus        81 ~vPS~~~~~~~AnW~ERE~YDmyGI~F~gHPdLrRil~P~df~G~hPLRKDyPl~g  136 (136)
T TIGR01961        81 HVPSVTSVFKTANWYERETYDMYGIVFDGHPDLRRILMPDDFEGVHPLRKDYPLTG  136 (136)
T ss_pred             CCCEEEECCCCCCCCCCEEEEEECCEECCCCCCCEEECCCCCEECCCCCCCCCCCC
T ss_conf             68701421467872220345431325737899753226888883257755677889


No 6  
>PRK08491 NADH dehydrogenase subunit C; Provisional
Probab=100.00  E-value=0  Score=388.06  Aligned_cols=132  Identities=30%  Similarity=0.582  Sum_probs=127.8

Q ss_pred             CEEEEEEECCCEEEEECHHHHHHHHHHHHHCCCCCCCEEEECCCCCCCCCCCCEEEEEEEEECCCCCEEEEEEEECCCCE
Q ss_conf             11457984795999986898999999987187898014751325688777785799999661575205998212057850
Q gi|254780854|r   19 SVRFAVNSVGELSLDVDCGDLVSLCSFLRDDPHCCFVNIIDLCGVDFLSRSNRFDVVYHFLSPKYNRRLRVKIAVAEGKS   98 (202)
Q Consensus        19 ~I~~~~~~~~el~i~V~~~~l~~vl~~LKdd~~~~F~~LiDItaVDyp~~~~RFeVvY~LlS~~~n~ri~Vk~~v~e~~~   98 (202)
                      .|.++.+..|++++.|+++++.+++++||   .|+|++|+|+||||||++.+||||||||||+++|.|||||+.++++++
T Consensus        48 ~i~~syie~~~lvi~i~~~dn~~~l~~Lk---~lgy~~Lse~sAiD~~~~~~rFEvvY~LLS~~~n~RiRvK~~v~e~e~  124 (263)
T PRK08491         48 EILDSYVELDQAVIWIKKDDNFKVLKILK---TLGYEILSEMSAIDFLAKKGGFEVFYQLLNLSKRKRVRVKCFVKKGEA  124 (263)
T ss_pred             HHHHHHHCCCEEEEEECHHHHHHHHHHHH---HCCHHHHHHHHCCCCCCCCCCEEEEEECCCCCCCCEEEEEEECCCCCC
T ss_conf             68887741572899975478899999998---778145333111444466895699998125666854999998689996


Q ss_pred             EECCCCCEECCCCEECCCHHHCCCEECCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             1012233025531011210113827356798767788998987871133778984
Q gi|254780854|r   99 VPSIVGIYPGADWFEREVWDMYGIFFEGHPDLRRILTDYGFEGHPLRKDFPVTGF  153 (202)
Q Consensus        99 vpSi~~i~p~A~W~ERE~~DmfGI~F~gHPdlRRiL~d~~feGhPLRKDFPltG~  153 (202)
                      ||||++||+||||+|||+||||||.|+||||||||||||||+||||||||||||=
T Consensus       125 i~Svt~i~~sAnW~ERE~yDmfGI~F~gHPdLrRILt~~~f~GhPLRKDfPL~GD  179 (263)
T PRK08491        125 LDSVSFLFRSANWSEREMYDMFGIVFNNHPYLKRILMPDDWVGHPLLKSYPLKGD  179 (263)
T ss_pred             CCCHHHHCCCCCHHHHHHHHHCCEEECCCCCCCEECCCCCCCCCCCCCCCCCCCC
T ss_conf             8725652245874888676442652479997120267889888861577788850


No 7  
>PRK11742 bifunctional NADH:ubiquinone oxidoreductase subunit C/D; Provisional
Probab=100.00  E-value=0  Score=344.42  Aligned_cols=143  Identities=41%  Similarity=0.734  Sum_probs=130.8

Q ss_pred             HHHHHHHCCCCEEEEEEE-CCCEEEEECHHHHHHHHHHHHHCCCCCCCEEEECCCCCCCCCCCC-------EEEEEEEEE
Q ss_conf             999998615311457984-795999986898999999987187898014751325688777785-------799999661
Q gi|254780854|r    9 GDYIVNSFSGSVRFAVNS-VGELSLDVDCGDLVSLCSFLRDDPHCCFVNIIDLCGVDFLSRSNR-------FDVVYHFLS   80 (202)
Q Consensus         9 ~~~L~~~l~~~I~~~~~~-~~el~i~V~~~~l~~vl~~LKdd~~~~F~~LiDItaVDyp~~~~R-------FeVvY~LlS   80 (202)
                      .+.|.++||+.+...+.. .+.+++.|+++.+.+||+|||+++ ++|.+|+|||||||+.+..|       |+|||||+|
T Consensus         2 ~~~L~~~Fg~~~~~~~~~~~~~~~~~v~~~~~~~v~~~L~~~~-~~f~~L~dl~~vD~~~r~~r~~~~~~~f~vvyhl~s   80 (575)
T PRK11742          2 IGELRNRFGPDAFTVQATRTGVPVVWIKREQLLEVLRFLRKLP-KPYVMLFDLHGIDERLRTHREGLPAADFTVFYHLIS   80 (575)
T ss_pred             HHHHHHHHCHHHCCEEECCCCCEEEEECHHHHHHHHHHHHCCC-CCCCCEEEEEEECCCCCCCCCCCCCCCEEEEEEEEE
T ss_conf             3789866123423101112895699986888999999985385-103501244554153334556688787799999863


Q ss_pred             CCCCCEEEEEEEECCCCE-EECCCCCEECCCCEECCCHHHCCCEECCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             575205998212057850-101223302553101121011382735679876778899898787113377898
Q gi|254780854|r   81 PKYNRRLRVKIAVAEGKS-VPSIVGIYPGADWFEREVWDMYGIFFEGHPDLRRILTDYGFEGHPLRKDFPVTG  152 (202)
Q Consensus        81 ~~~n~ri~Vk~~v~e~~~-vpSi~~i~p~A~W~ERE~~DmfGI~F~gHPdlRRiL~d~~feGhPLRKDFPltG  152 (202)
                      +++|.||+||+.++++.+ +|||+++||+|||||||+||||||.|+|||||||||++++|+|||||||||..+
T Consensus        81 ~~~n~~irvk~~~~~~~~~~~s~~~~~~~a~w~Ere~~d~~Gi~f~ghp~~rr~~~~~~~~~~plrkd~~~~~  153 (575)
T PRK11742         81 IERNRDIMLKVALSENDLRVPTITKIFPNANWYERETWDMFGITFDGHPHLRRILMPPTWEGHPLRKDYPARA  153 (575)
T ss_pred             CCCCCEEEEEEECCCCCCCCCCHHHHCCCCCHHHHHHHHHCCCCCCCCCCCCCEECCCCCCCCCCCCCCCCCC
T ss_conf             6889669999865787898981566333675788888762386637999862121677678888767775445


No 8  
>PRK13292 trifunctional NADH dehydrogenase I subunit B/C/D; Provisional
Probab=100.00  E-value=0  Score=310.67  Aligned_cols=147  Identities=36%  Similarity=0.623  Sum_probs=136.3

Q ss_pred             HHHHHHHHHCCCCEEEEEEECCCEEEEECHHHHHHHHHHHHHCCCCCCCEEEECCCCCCCCCCCC-----EEEEEEEEEC
Q ss_conf             99999998615311457984795999986898999999987187898014751325688777785-----7999996615
Q gi|254780854|r    7 DLGDYIVNSFSGSVRFAVNSVGELSLDVDCGDLVSLCSFLRDDPHCCFVNIIDLCGVDFLSRSNR-----FDVVYHFLSP   81 (202)
Q Consensus         7 ~L~~~L~~~l~~~I~~~~~~~~el~i~V~~~~l~~vl~~LKdd~~~~F~~LiDItaVDyp~~~~R-----FeVvY~LlS~   81 (202)
                      +|+..|++.|++.+.......+.+++.|+++.+.+++++||++.+.+|++|.||||||++.+.+|     |.|||||+|+
T Consensus       219 ~~~~~l~~~~~~~~~~~~~~~~~~t~~~~~~~~~~~~~~lk~~~~~~f~~l~~i~~vD~~~~~~~~~~~~~~~~y~l~s~  298 (784)
T PRK13292        219 GLAGELEEAFGDRVRVEEFATDMLTYRCPPELVPEVLRHLKQRSSAPFRRLEDLAAVDESCRRERSAFPDFTVNYHLLSF  298 (784)
T ss_pred             HHHHHHHHHHCCCEEECCCCCCCEEEECCHHHHHHHHHHHHHCCCCCCHHHCCCEEECCCCCCCCCCCCCEEEEEEEECC
T ss_conf             58899998726544651465663256347777799999986555644201025211102011366667855899996124


Q ss_pred             CCCCEEEEEEEECC-CCEEECCCCCEECCCCEECCCHHHCCCEECCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             75205998212057-8501012233025531011210113827356798767788998987871133778984
Q gi|254780854|r   82 KYNRRLRVKIAVAE-GKSVPSIVGIYPGADWFEREVWDMYGIFFEGHPDLRRILTDYGFEGHPLRKDFPVTGF  153 (202)
Q Consensus        82 ~~n~ri~Vk~~v~e-~~~vpSi~~i~p~A~W~ERE~~DmfGI~F~gHPdlRRiL~d~~feGhPLRKDFPltG~  153 (202)
                      +.|..++||+.+++ ++.+|||+++||+|||||||+||||||.|.||||+||||++.+|+|||||||||..-.
T Consensus       299 ~~~~~~~~~~~~~~~~p~~psi~~~~p~a~w~ErE~~d~fGi~f~ghp~~rr~~l~~~~~~~PlrKD~~~~~~  371 (784)
T PRK13292        299 DTPGHLRIKTELRGDTPELPSITGVFPAANWYEREAFDMFGIRFAGHPNLRRILMPPDWEGHPLRKEHPFRAT  371 (784)
T ss_pred             CCCCEEEEEEECCCCCCCCCCHHHHCCCCCHHHHHHHHHCCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCC
T ss_conf             6786589983168778999835663347752888888743714369988412358998999986678877666


No 9  
>CHL00012 ndhJ NADH dehydrogenase subunit J
Probab=100.00  E-value=5.6e-45  Score=295.30  Aligned_cols=126  Identities=30%  Similarity=0.540  Sum_probs=117.0

Q ss_pred             CCEEEEECHHHHHHHHHHHHHCCCCCCCEEEECCCCCCCCCCCCEEEEEEEEECCCC----CEEEEEEEECC-CCEEECC
Q ss_conf             959999868989999999871878980147513256887777857999996615752----05998212057-8501012
Q gi|254780854|r   28 GELSLDVDCGDLVSLCSFLRDDPHCCFVNIIDLCGVDFLSRSNRFDVVYHFLSPKYN----RRLRVKIAVAE-GKSVPSI  102 (202)
Q Consensus        28 ~el~i~V~~~~l~~vl~~LKdd~~~~F~~LiDItaVDyp~~~~RFeVvY~LlS~~~n----~ri~Vk~~v~e-~~~vpSi  102 (202)
                      |--+|.|++++|..|+..|+..   +|++|.+.||.|+.. .+++..||||.|+..+    .|||||+.+++ ++.||||
T Consensus        25 GvE~i~v~~~~~~~va~aL~~~---GFnyL~~q~gyD~~p-g~~l~svYhl~~~~~~~d~p~rvrlKV~lpre~P~vPSv  100 (158)
T CHL00012         25 GIETLQIKPEDWHSIAVILYVY---GYNYLRSQCAYDVAP-GGLLASVYHLTRIEYGVDQPEEVCIKVFVPRDNPRIPSV  100 (158)
T ss_pred             CEEEEEECHHHHHHHHHHHHHH---CCCCEEEEEEECCCC-CCCEEEEEEEEEECCCCCCCCEEEEEEECCCCCCCCCCC
T ss_conf             5378766676869999999981---854124663231379-985799999988125656786799999657889989978


Q ss_pred             CCCEECCCCEECCCHHHCCCEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEE
Q ss_conf             2330255310112101138273567987677889989878711337789844788
Q gi|254780854|r  103 VGIYPGADWFEREVWDMYGIFFEGHPDLRRILTDYGFEGHPLRKDFPVTGFVELH  157 (202)
Q Consensus       103 ~~i~p~A~W~ERE~~DmfGI~F~gHPdlRRiL~d~~feGhPLRKDFPltG~~evr  157 (202)
                      ++|||||||+|||+||||||.|+|||||||||++++|+|||||||||++||.|++
T Consensus       101 ~~iwp~Adw~ERE~~DmfGI~F~GHPdlrRillpdd~~g~PLRKDf~~p~~~elq  155 (158)
T CHL00012        101 FWVWKSADFQERESYDMLGISYDNHPRLKRILMPESWIGWPLRKDYIAPNFYEIQ  155 (158)
T ss_pred             HHCCCCCEEEHHHHHHHCCEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEE
T ss_conf             0001486442554554408013699996211489999988854650699935721


No 10 
>PRK12494 NADH dehydrogenase subunit J; Provisional
Probab=100.00  E-value=1.8e-42  Score=279.67  Aligned_cols=124  Identities=37%  Similarity=0.592  Sum_probs=115.0

Q ss_pred             EEEEECHHHHHHHHHHHHHCCCCCCCEEEECCCCCCCCCCCCEEEEEEEEECCCC----CEEEEEEEECC-CCEEECCCC
Q ss_conf             9999868989999999871878980147513256887777857999996615752----05998212057-850101223
Q gi|254780854|r   30 LSLDVDCGDLVSLCSFLRDDPHCCFVNIIDLCGVDFLSRSNRFDVVYHFLSPKYN----RRLRVKIAVAE-GKSVPSIVG  104 (202)
Q Consensus        30 l~i~V~~~~l~~vl~~LKdd~~~~F~~LiDItaVDyp~~~~RFeVvY~LlS~~~n----~ri~Vk~~v~e-~~~vpSi~~  104 (202)
                      -+|.|+++.|..++..|+..   +|++|.+.||+|... .+++..||||.|+..+    .+||||+.+++ ++.||||++
T Consensus        41 E~i~V~p~~l~~va~aL~~~---GFnyL~~q~~yD~~P-g~~LvsvYHl~~~~d~~d~p~evrlKV~vprd~P~iPSi~~  116 (172)
T PRK12494         41 EIIKVEPDFLLPIATALYAY---GFNYLQCQGGYDEGP-GKNLVSFYHLIKVSDNADKPREVRLKVFLPRDDPRVPSVYW  116 (172)
T ss_pred             EEEEECHHHHHHHHHHHHHC---CCCHHHHEEEEECCC-CCEEEEEEEEEEECCCCCCCCEEEEEEECCCCCCCCCCHHH
T ss_conf             77314789999999999982---850000110263279-97489998577842676787689999977888998997366


Q ss_pred             CEECCCCEECCCHHHCCCEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEE
Q ss_conf             30255310112101138273567987677889989878711337789844788
Q gi|254780854|r  105 IYPGADWFEREVWDMYGIFFEGHPDLRRILTDYGFEGHPLRKDFPVTGFVELH  157 (202)
Q Consensus       105 i~p~A~W~ERE~~DmfGI~F~gHPdlRRiL~d~~feGhPLRKDFPltG~~evr  157 (202)
                      |||+|||+|||+||||||.|+|||||||||++++|+||||||||++.+|.|++
T Consensus       117 iw~~AdW~ERE~yDmfGI~F~GHPdlrRilmpedw~G~PLRKDyi~pdfyelq  169 (172)
T PRK12494        117 IWKGADWQERETYDMYGINFEGHPNLKRILMPEDWVGWPLRKDYIQPDFYELQ  169 (172)
T ss_pred             HCCCCCCHHHHHHHHCCEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEE
T ss_conf             15588501543421047364799986035699999888866772699840410


No 11 
>PRK07735 NADH dehydrogenase subunit C; Validated
Probab=100.00  E-value=2.8e-41  Score=272.40  Aligned_cols=141  Identities=30%  Similarity=0.516  Sum_probs=127.2

Q ss_pred             HHHHHHHHHHHCCCCEEE-EE---EECCCEEEEECHHHHHHHHHHHHHCCCCCCCEEEECCCCCCCCCCCCEEEEEEEEE
Q ss_conf             999999999861531145-79---84795999986898999999987187898014751325688777785799999661
Q gi|254780854|r    5 IEDLGDYIVNSFSGSVRF-AV---NSVGELSLDVDCGDLVSLCSFLRDDPHCCFVNIIDLCGVDFLSRSNRFDVVYHFLS   80 (202)
Q Consensus         5 L~~L~~~L~~~l~~~I~~-~~---~~~~el~i~V~~~~l~~vl~~LKdd~~~~F~~LiDItaVDyp~~~~RFeVvY~LlS   80 (202)
                      |+.+.+.|.+.++..+.. ..   ...+-.++.|.++.+.+|+.+||.|+++.|++|+.+.|+||-   .+.||+|||.|
T Consensus       268 L~~yv~vi~e~~g~~vl~d~YIN~LskdvPtlvv~~e~yy~v~E~lr~hE~l~fdYlSeLh~tDf~---thmEvyvHl~S  344 (420)
T PRK07735        268 LNQYVEVIKEKLGEDALVDAYINKLSKDVPTLVVEPEKYYEVMELLRFHEGLAFDYMSELHATDFV---THMEVYVHLFS  344 (420)
T ss_pred             HHHHHHHHHHHCCHHHHHHHHHHHHCCCCCEEEECHHHHHHHHHHHHHHHCCCHHHHHHHHCCCHH---HHEEEEEEEEE
T ss_conf             999999999870147899999988606688157545879999999875031024788763030024---11056787775


Q ss_pred             CCCCCEEEEEEEECC-CCEEECCCCCEECCCCEECCCHHHCCCEECCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             575205998212057-85010122330255310112101138273567987677889989878711337
Q gi|254780854|r   81 PKYNRRLRVKIAVAE-GKSVPSIVGIYPGADWFEREVWDMYGIFFEGHPDLRRILTDYGFEGHPLRKDF  148 (202)
Q Consensus        81 ~~~n~ri~Vk~~v~e-~~~vpSi~~i~p~A~W~ERE~~DmfGI~F~gHPdlRRiL~d~~feGhPLRKDF  148 (202)
                      +.+.+.+.|||.++. +|.|+||+++|+||||-|||+|||+||.|.|||||+|||++++|.||||||||
T Consensus       345 y~~rq~vavKVK~dRe~p~v~Sv~plW~gAnWpErEayDLLGi~F~GHpnL~RI~mpddWvGhPLRKDY  413 (420)
T PRK07735        345 YGKKQSVAVKVKLDREAPQVESVTPLWKGADWPEREAYDLLGIVFKGHPNLSRILMPDDWVGHPLRKDY  413 (420)
T ss_pred             CCCCCEEEEEEECCCCCCCCCCHHCCCCCCCCCHHHHHHHHCCCCCCCCCCEEEECCCCCCCCCCCCCC
T ss_conf             278861689863145676543100135789983455665402112699880001166444578433557


No 12 
>pfam00329 Complex1_30kDa Respiratory-chain NADH dehydrogenase, 30 Kd subunit.
Probab=100.00  E-value=6.9e-38  Score=251.78  Aligned_cols=102  Identities=50%  Similarity=0.992  Sum_probs=95.6

Q ss_pred             HHHHHHHHCCCCCCCEEEECCCCCCCCCCCCEEEEEEEEECCCCCEEEEEEEEC-CCCEEECCCCCEECCCCEECCCHHH
Q ss_conf             999998718789801475132568877778579999966157520599821205-7850101223302553101121011
Q gi|254780854|r   41 SLCSFLRDDPHCCFVNIIDLCGVDFLSRSNRFDVVYHFLSPKYNRRLRVKIAVA-EGKSVPSIVGIYPGADWFEREVWDM  119 (202)
Q Consensus        41 ~vl~~LKdd~~~~F~~LiDItaVDyp~~~~RFeVvY~LlS~~~n~ri~Vk~~v~-e~~~vpSi~~i~p~A~W~ERE~~Dm  119 (202)
                      +++.+||++   +|.+|++|||+||++. ++|+++|||.|...+.+++||+.++ +++.||||++|||+|+|+|||+|||
T Consensus         1 ~~~~~l~~~---g~~~L~~i~~~D~~~~-~~~~~~Y~~~~~~~~~~v~l~~~v~~~~p~vpSi~~i~p~A~w~ERE~~Dm   76 (103)
T pfam00329         1 EVARFLKED---GFDRLSDLTGVDYPEE-GRFEVVYHLASIGDGERVRLKVKLPRDDPEIPSITDIFPGANWYEREVYDM   76 (103)
T ss_pred             CHHHHHHHC---CCCEEEEEEEEECCCC-CEEEEEEEEEECCCCCEEEEEEEECCCCCCCCCCCCCEECCCHHHHHHHEE
T ss_conf             977999768---9995878886988999-989999999978899499999993887871385312275788877223161


Q ss_pred             CCCEECCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             382735679876778899898787113
Q gi|254780854|r  120 YGIFFEGHPDLRRILTDYGFEGHPLRK  146 (202)
Q Consensus       120 fGI~F~gHPdlRRiL~d~~feGhPLRK  146 (202)
                      |||.|+||||+||||++++|+||||||
T Consensus        77 fGi~f~ghPd~rrlll~~~~~~~PLrK  103 (103)
T pfam00329        77 FGIVFEGHPDLRRLLLPEDWPGHPLRK  103 (103)
T ss_pred             CCEEECCCCCCCCCCCCCCCCCCCCCC
T ss_conf             263768999972414888998998789


No 13 
>COG3262 HycE Ni,Fe-hydrogenase III component G [Energy production and conversion]
Probab=99.95  E-value=1.8e-27  Score=188.35  Aligned_cols=144  Identities=34%  Similarity=0.461  Sum_probs=113.3

Q ss_pred             CCH-HHHHHHHHHHHHCCCCEEEE-EEECCCEEEEECHHHHHHHHHHHHHCCCCCCCEEEECCCCCCCCCCCCEEEEEEE
Q ss_conf             905-79999999998615311457-9847959999868989999999871878980147513256887777857999996
Q gi|254780854|r    1 MVR-KIEDLGDYIVNSFSGSVRFA-VNSVGELSLDVDCGDLVSLCSFLRDDPHCCFVNIIDLCGVDFLSRSNRFDVVYHF   78 (202)
Q Consensus         1 M~~-~L~~L~~~L~~~l~~~I~~~-~~~~~el~i~V~~~~l~~vl~~LKdd~~~~F~~LiDItaVDyp~~~~RFeVvY~L   78 (202)
                      |++ ..+.+...|.+.|++.|... .....++++.|..+.+.+++++|+...+ .+  +.-+.|.|.-..+..| .||.|
T Consensus         1 ~~e~k~e~~~~el~~~fpg~i~~e~~~~~~~~~~~V~~~~l~~~~e~l~~~~d-~~--~~~liG~~e~~~~~~~-~v~~f   76 (165)
T COG3262           1 SEEVKGEEILAELNERFPGVVLDEERQTRSQLTVTVKREYLPDVVEFLYYELD-GW--LSVLIGNDEDALNGHF-AVYLF   76 (165)
T ss_pred             CCCHHHHHHHHHHHHHCCCHHHHHHHHCHHHEEEEEEHHHHHHHHHHHHHHHC-CC--HHEEECCCCCCCCCCE-EEEEE
T ss_conf             93136789999999767404134303052141676448662999999987606-53--3001313444446731-69999


Q ss_pred             EECCCC--CEEEEEEEECC-CCEEECCCCCEECCCCEECCCHHHCCCEECCCCCCCCCC-CCCCCCC-CCCCCCC
Q ss_conf             615752--05998212057-850101223302553101121011382735679876778-8998987-8711337
Q gi|254780854|r   79 LSPKYN--RRLRVKIAVAE-GKSVPSIVGIYPGADWFEREVWDMYGIFFEGHPDLRRIL-TDYGFEG-HPLRKDF  148 (202)
Q Consensus        79 lS~~~n--~ri~Vk~~v~e-~~~vpSi~~i~p~A~W~ERE~~DmfGI~F~gHPdlRRiL-~d~~feG-hPLRKDF  148 (202)
                      ||++..  .++.||+.++. ++.+|||++|+|+|.|+|||+-|||||.|.||||.||+. .|.+.|| ||||||+
T Consensus        77 Ls~~~a~~~~v~vk~~vp~dnpe~pSva~i~P~A~wfEREi~Dm~Gl~~vg~PD~RRLvLpddwPeg~yPLRkd~  151 (165)
T COG3262          77 LSMEQAPKCWVIVKVSVPADNPEFPSVAPIFPAALWFEREIRDMYGLDPVGAPDPRRLVLPDDWPEGIYPLRKDA  151 (165)
T ss_pred             EEECCCCCEEEEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCEEECCCCCCCCCCCCHHHC
T ss_conf             987168974899998628989867763102650478899999861856378998530435544766643001213


No 14 
>PRK02224 chromosome segregation protein; Provisional
Probab=42.88  E-value=30  Score=16.51  Aligned_cols=18  Identities=17%  Similarity=0.093  Sum_probs=11.3

Q ss_pred             EECCCCEECCCHHHCCCE
Q ss_conf             025531011210113827
Q gi|254780854|r  106 YPGADWFEREVWDMYGIF  123 (202)
Q Consensus       106 ~p~A~W~ERE~~DmfGI~  123 (202)
                      +.++.--.+++-+++|+.
T Consensus       108 ~~~~~~v~~~i~~ilg~~  125 (880)
T PRK02224        108 IDGATDVYAEITELLRMD  125 (880)
T ss_pred             ECCHHHHHHHHHHHHCCC
T ss_conf             025578999999996998


No 15 
>PRK06452 sdhA succinate dehydrogenase flavoprotein subunit; Reviewed
Probab=41.01  E-value=25  Score=16.97  Aligned_cols=18  Identities=6%  Similarity=-0.055  Sum_probs=6.5

Q ss_pred             CCCEEEECCCCCCCCCCC
Q ss_conf             801475132568877778
Q gi|254780854|r   53 CFVNIIDLCGVDFLSRSN   70 (202)
Q Consensus        53 ~F~~LiDItaVDyp~~~~   70 (202)
                      +-+.+....++|....++
T Consensus       150 ~i~~~~~~~~~~Ll~~~~  167 (566)
T PRK06452        150 NVDFYNEWFAWDLVRDEK  167 (566)
T ss_pred             CCEEEEEEEEEEEEECCC
T ss_conf             978998789999885398


No 16 
>TIGR00538 hemN oxygen-independent coproporphyrinogen III oxidase; InterPro: IPR004558   This family represents HemN, the oxygen-independent coproporphyrinogen III oxidase that replaces HemF function under anaerobic conditions. HemN catalyses the anaerobic transformation of coproporhyrinogen-III into protoporphyrinogen-IX during porphyrin biosynthesis. Several species, including Escherichia coli, Helicobacter pylori, and Aquifex aeolicus, have both a member of this family and a member of another, closely related family for which there is no evidence of coproporphyrinogen III oxidase activity, IPR004559 from INTERPRO. Members of this family have a perfectly conserved motif PYRT[SC]YP in a region N-terminal to the region of homology with the related uncharacterised protein.; GO: 0004109 coproporphyrinogen oxidase activity, 0006779 porphyrin biosynthetic process, 0005737 cytoplasm.
Probab=40.76  E-value=32  Score=16.30  Aligned_cols=53  Identities=32%  Similarity=0.463  Sum_probs=41.4

Q ss_pred             HHHHHHHHHHHHHCCCCEEEEEEECCCEEEEECHHHH-HHHHHHHHHCCCCCCCEEEECCCC-CC
Q ss_conf             5799999999986153114579847959999868989-999999871878980147513256-88
Q gi|254780854|r    3 RKIEDLGDYIVNSFSGSVRFAVNSVGELSLDVDCGDL-VSLCSFLRDDPHCCFVNIIDLCGV-DF   65 (202)
Q Consensus         3 ~~L~~L~~~L~~~l~~~I~~~~~~~~el~i~V~~~~l-~~vl~~LKdd~~~~F~~LiDItaV-Dy   65 (202)
                      ++++.|-+.|.+.|+.--     ..-|+.|.|+|-.+ .+.+..||+.   ||+-|+  -|| |+
T Consensus       121 ~Q~~~l~~~i~~~F~nf~-----~daEiSiEidPR~~~~e~~~~L~~~---GFNRlS--~GvQDf  175 (462)
T TIGR00538       121 EQIEELMKEIREAFPNFS-----EDAEISIEIDPRYLTKEVIKALRDE---GFNRLS--FGVQDF  175 (462)
T ss_pred             HHHHHHHHHHHHHHHHHC-----CCCEEEEEECCCCCCHHHHHHHHHC---CCCEEE--CCEECC
T ss_conf             999999999998732011-----5844776523741378899999975---896642--352107


No 17 
>PRK05253 sulfate adenylyltransferase subunit 2; Provisional
Probab=38.90  E-value=13  Score=18.77  Aligned_cols=111  Identities=22%  Similarity=0.396  Sum_probs=53.1

Q ss_pred             CHHHHHHHHHHHHHCCCCCCCEEEECCCCCCCCCCCCE-EEEEEEEE----C-CCCCEEEE----EEEECCCCEEECCCC
Q ss_conf             68989999999871878980147513256887777857-99999661----5-75205998----212057850101223
Q gi|254780854|r   35 DCGDLVSLCSFLRDDPHCCFVNIIDLCGVDFLSRSNRF-DVVYHFLS----P-KYNRRLRV----KIAVAEGKSVPSIVG  104 (202)
Q Consensus        35 ~~~~l~~vl~~LKdd~~~~F~~LiDItaVDyp~~~~RF-eVvY~LlS----~-~~n~ri~V----k~~v~e~~~vpSi~~  104 (202)
                      ..-+...+...|.   ..+|+-+  ++|+-.=+...|= |-++-+-+    + -.|+|--+    ++....++    -.-
T Consensus       111 ~~lKT~~L~~al~---~~~fda~--~gGaRRDEe~sRAKERiFS~R~~~~~Wdpk~QrPElW~lyn~~~~~ge----h~R  181 (300)
T PRK05253        111 NIMKTEGLKQALE---KYGFDAA--FGGARRDEEKSRAKERIFSFRDEFGQWDPKNQRPELWNLYNGRINKGE----HIR  181 (300)
T ss_pred             HHHHHHHHHHHHH---HCCCCEE--EECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHCCCCCCCC----EEE
T ss_conf             5787899999999---6487656--510123443212125424775646888856698026676355679996----477


Q ss_pred             CEECCCCEECCCHH--------HCCCEECCC-CCCCC---CCCCCCCCCCCCCC---------------CCCCCCCEEE
Q ss_conf             30255310112101--------138273567-98767---78899898787113---------------3778984478
Q gi|254780854|r  105 IYPGADWFEREVWD--------MYGIFFEGH-PDLRR---ILTDYGFEGHPLRK---------------DFPVTGFVEL  156 (202)
Q Consensus       105 i~p~A~W~ERE~~D--------mfGI~F~gH-PdlRR---iL~d~~feGhPLRK---------------DFPltG~~ev  156 (202)
                      +||-.||-|..+|.        .--++|.-. |-..|   +++-.++  .||+.               |.|+||-+|-
T Consensus       182 VfPlsnWTElDIW~YI~~E~Ipi~~LYfA~~r~vv~r~g~l~~~dd~--~~~~~~e~~~~~~vRfRTLGc~p~TgaveS  258 (300)
T PRK05253        182 VFPLSNWTELDIWQYIYRENIPIVPLYFAHERPVVERDGMLIMVDDD--MPLRPGEVVEERMVRFRTLGCYPCTGAVES  258 (300)
T ss_pred             EECCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCEEEECCEEEECCCC--CCCCCCCEEEECCCEECCCCCCCCCCCCCC
T ss_conf             51120225778999999848888871103788548789988743866--677999835334501224677456784157


No 18 
>pfam00828 Ribosomal_L18e Ribosomal protein L18e/L15. This family includes eukaryotic L18 as well as prokaryotic L15.
Probab=37.09  E-value=9.8  Score=19.43  Aligned_cols=34  Identities=32%  Similarity=0.439  Sum_probs=25.6

Q ss_pred             CCCC--CCCCCCCCCCCCEEEEECHHHCEEECCCCEEEEH
Q ss_conf             8987--8711337789844788762115131266422022
Q gi|254780854|r  138 GFEG--HPLRKDFPVTGFVELHYDDKVKKVVYRPVELMQE  175 (202)
Q Consensus       138 ~feG--hPLRKDFPltG~~evryd~~~k~v~~epv~l~q~  175 (202)
                      +|||  .||-+.+|=-||.-.    ...+..|.||+|.+=
T Consensus        24 ~FeGGq~pl~rrlpKrGf~~~----~~~~~~~~~inL~~l   59 (122)
T pfam00828        24 PFEGGQVPLYRRLGKRGFRRL----FKSRKNRPPVNLSKL   59 (122)
T ss_pred             CCCCCCCHHHHHHCCCCCCCC----CCCCEEEEEEEHHHH
T ss_conf             864686613443321476665----667518999889995


No 19 
>TIGR02166 dmsA_ynfE anaerobic dimethyl sulfoxide reductase,  A subunit, DmsA/YnfE family; InterPro: IPR011888   Many bacterial species are capable of anaerobic growth by using dimethylsulphoxide (DMSO) as the terminal electron acceptor, with DMSO reductase as the terminal elctron transfer enzyme. In Escherichia coli and many other Gram-negative bacteria DMSO reductase is a membrane-bound enzyme composed of three subunits; a catalytic molybdenum-containing subunit (DmsA), an electron transfer subunit containing a [4Fe-4S] cluster (DmsB), and a hydrophobic membrane-spanning anchor subunit which attaches the enzyme to the cytoplasmic membrane (DmsC) , . It is generally thought now that DmsAB faces the periplasm, contradicting previous results suggesting a cytoplasmic location. The N-terminal region of DmsA contains a "twin-arginine" signal sequence, suggesting export to the periplasm occurs via the TAT secretion pathway.   This entry represents known and predicted bacterial DmsA polypeptides. Several species contain one or more paralogs of DmsA. In E. coli, the two paralogs of DmsA, YnfE and YnfF, are encoded within the ynfEFGHI operon . YnfE and YnfF cannot form a functional complex with DmsBC, but YnfFGH can restore growth on DMSO when DmABC is deleted. The function of YnfE is not known and it appears to prevent formation of the YnfFGH complex if present.; GO: 0009389 dimethyl sulfoxide reductase activity, 0030151 molybdenum ion binding, 0051539 4 iron 4 sulfur cluster binding.
Probab=36.16  E-value=14  Score=18.54  Aligned_cols=69  Identities=28%  Similarity=0.418  Sum_probs=34.5

Q ss_pred             EEEEEECCCCCEEEEEEEEC--CCCEEECC---CCCEECCCCEECCCHHHCCCEECCCCC--CCCC--CCCC--CCCCC-
Q ss_conf             99966157520599821205--78501012---233025531011210113827356798--7677--8899--89878-
Q gi|254780854|r   75 VYHFLSPKYNRRLRVKIAVA--EGKSVPSI---VGIYPGADWFEREVWDMYGIFFEGHPD--LRRI--LTDY--GFEGH-  142 (202)
Q Consensus        75 vY~LlS~~~n~ri~Vk~~v~--e~~~vpSi---~~i~p~A~W~ERE~~DmfGI~F~gHPd--lRRi--L~d~--~feGh-  142 (202)
                      +|..-+-.. +.|..+-+++  ++.|++|=   .-||..+--.=-+.|.+       .|+  =-+|  |.-|  .|||+ 
T Consensus       642 ~~~~~~~~~-~~vA~~~f~~dPeanPl~TPSGKIEIYS~~LA~~~~~W~l-------~~nvkg~~Italp~Y~pt~EG~~  713 (849)
T TIGR02166       642 IYKAKSAKG-PFVAFEDFRRDPEANPLKTPSGKIEIYSERLAQIAHTWEL-------PENVKGDEITALPEYVPTFEGYD  713 (849)
T ss_pred             CEECCCCCC-CEEEEHHHHCCCCCCCCCCCCCCEEHHHHHHHHHHHCCCC-------CCCCCCCCCCCCCEEECCCCCCC
T ss_conf             310137898-6675212105865677786785254546999876630788-------87778873576540108888888


Q ss_pred             -CC-CCCCCCC
Q ss_conf             -71-1337789
Q gi|254780854|r  143 -PL-RKDFPVT  151 (202)
Q Consensus       143 -PL-RKDFPlt  151 (202)
                       |+ ||||||.
T Consensus       714 D~~T~~~fPLQ  724 (849)
T TIGR02166       714 DPETRKDFPLQ  724 (849)
T ss_pred             CHHHHHCCCCC
T ss_conf             86665158741


No 20 
>KOG1372 consensus
Probab=35.64  E-value=15  Score=18.29  Aligned_cols=20  Identities=45%  Similarity=0.833  Sum_probs=16.3

Q ss_pred             ECCCHHHC---CCEECCCCCCCCC
Q ss_conf             11210113---8273567987677
Q gi|254780854|r  113 EREVWDMY---GIFFEGHPDLRRI  133 (202)
Q Consensus       113 ERE~~Dmf---GI~F~gHPdlRRi  133 (202)
                      =||+|.||   ||.| ||.-.||=
T Consensus       198 yREAYnmfAcNGILF-NHESPRRG  220 (376)
T KOG1372         198 YREAYNMFACNGILF-NHESPRRG  220 (376)
T ss_pred             HHHHHCCEEECCEEE-CCCCCCCC
T ss_conf             488412013131765-47787666


No 21 
>pfam01305 consensus
Probab=32.90  E-value=14  Score=18.55  Aligned_cols=33  Identities=39%  Similarity=0.737  Sum_probs=27.1

Q ss_pred             CCCCC--CCCCCCCCCCCCEEEEECHHHCEEECCCCEEEEH
Q ss_conf             98987--8711337789844788762115131266422022
Q gi|254780854|r  137 YGFEG--HPLRKDFPVTGFVELHYDDKVKKVVYRPVELMQE  175 (202)
Q Consensus       137 ~~feG--hPLRKDFPltG~~evryd~~~k~v~~epv~l~q~  175 (202)
                      -+|||  -||-+-+|--||.      ...+..|++|+|.+=
T Consensus        48 ~gFEGGQ~Pl~rRlPKrGF~------n~~~~~~~~vnl~~L   82 (102)
T pfam01305        48 RGFEGGQTPLYRRLPKRGFT------NIKRKRYAEVNLKDL   82 (102)
T ss_pred             CCCCCCCCEEEEECCCCCCC------CCCCCEEEEEEHHHH
T ss_conf             74337874016725636767------888875588859998


No 22 
>pfam10364 NKWYS Putative capsular polysaccharide synthesis protein. Found only in Vibrio species, pombe and one other fungi, this is a the N-terminal 150 residues of a family of proteins of unknown function. There is a characteristic NKWYS sequence motif.
Probab=31.94  E-value=12  Score=18.98  Aligned_cols=25  Identities=20%  Similarity=0.404  Sum_probs=19.3

Q ss_pred             EECCCCEECCCHHHCCCEECCCCCC
Q ss_conf             0255310112101138273567987
Q gi|254780854|r  106 YPGADWFEREVWDMYGIFFEGHPDL  130 (202)
Q Consensus       106 ~p~A~W~ERE~~DmfGI~F~gHPdl  130 (202)
                      =-.++|+-||+-+.|||.--+||=-
T Consensus        31 ~y~l~WFD~Eik~~fGIDV~~~~F~   55 (141)
T pfam10364        31 NYALEWFDNEIKELFGIDVFNQDFD   55 (141)
T ss_pred             HHHHHHHHHHHHHHCCCEECCCCCC
T ss_conf             1267888999998719212057689


No 23 
>PRK12563 sulfate adenylyltransferase subunit 2; Provisional
Probab=31.86  E-value=16  Score=18.12  Aligned_cols=113  Identities=26%  Similarity=0.437  Sum_probs=53.0

Q ss_pred             HHHHHHHHHHHCCCCCCCEEEECCCCCCCCCCCC-EEEEEEEEECC-----CCCEEEE----EEEECCCCEEECCCCCEE
Q ss_conf             8999999987187898014751325688777785-79999966157-----5205998----212057850101223302
Q gi|254780854|r   38 DLVSLCSFLRDDPHCCFVNIIDLCGVDFLSRSNR-FDVVYHFLSPK-----YNRRLRV----KIAVAEGKSVPSIVGIYP  107 (202)
Q Consensus        38 ~l~~vl~~LKdd~~~~F~~LiDItaVDyp~~~~R-FeVvY~LlS~~-----~n~ri~V----k~~v~e~~~vpSi~~i~p  107 (202)
                      +...+.+.|.   ..+|+-+  +.|+-.=+..-| =|-++-+-+-.     .|+|--+    .+....++    -.-+||
T Consensus       125 KT~~L~~ale---~~~fDa~--~gGaRRDEEksRAKERiFS~Rd~~~~WDPknQrPElWnlyN~~~~~Ge----h~RVfP  195 (312)
T PRK12563        125 KTQGLKQALD---HHGFDAA--IGGARRDEEKSRAKERIFSFRSAFHRWDPKAQRPELWSLYNARLRRGE----SLRVFP  195 (312)
T ss_pred             HHHHHHHHHH---HCCCCEE--EECCCCCCCCCCCCCEEECCCCCCCCCCCCCCCHHHHHHHCCCCCCCC----EEEECC
T ss_conf             8899999999---7398878--504532134234434030666778898855588358776155679997----144223


Q ss_pred             CCCCEECCCHHH--------CCCEECCC-CCCCC--CCCCCCCCCCCCCC---------------CCCCCCCEEEEEC
Q ss_conf             553101121011--------38273567-98767--78899898787113---------------3778984478876
Q gi|254780854|r  108 GADWFEREVWDM--------YGIFFEGH-PDLRR--ILTDYGFEGHPLRK---------------DFPVTGFVELHYD  159 (202)
Q Consensus       108 ~A~W~ERE~~Dm--------fGI~F~gH-PdlRR--iL~d~~feGhPLRK---------------DFPltG~~evryd  159 (202)
                      -.||-|..+|.-        --++|..- |=.+|  .|...+=+-.||++               |.|+||-+|-.=+
T Consensus       196 lsNWTElDIW~YI~~E~Ipi~~LYFa~~R~vv~RdG~li~vdd~~~~l~~gE~~~~~~vRfRTLGc~p~TgaveS~A~  273 (312)
T PRK12563        196 LSNWTELDVWQYIAREKIPLVPLYFAKRRPVVERDGLLIMVDDERTPLRPGETPQQRKVRFRTLGCYPLTGAVESDAD  273 (312)
T ss_pred             CCCCCHHHHHHHHHHHCCCCCCCEECCCCCEEEECCEEEECCCCCCCCCCCCCCEECCEEEECCCCCCCCCCCCCCCC
T ss_conf             556617899999998288988612115664275589488357766678888843014421211566366782057888


No 24 
>COG1334 FlaG Uncharacterized flagellar protein FlaG [Cell motility and secretion]
Probab=30.71  E-value=47  Score=15.32  Aligned_cols=39  Identities=18%  Similarity=0.221  Sum_probs=23.3

Q ss_pred             CCCCEEEEEE-ECCCEEEEECHHHHHHHHHHHHHCCCCCC
Q ss_conf             1531145798-47959999868989999999871878980
Q gi|254780854|r   16 FSGSVRFAVN-SVGELSLDVDCGDLVSLCSFLRDDPHCCF   54 (202)
Q Consensus        16 l~~~I~~~~~-~~~el~i~V~~~~l~~vl~~LKdd~~~~F   54 (202)
                      ++..+..+.. ..|++.=.|+++.+.++++.|++.-+.-|
T Consensus        77 lg~~vVkI~d~~TgeVIRqIPpee~L~l~~r~~d~~gil~  116 (120)
T COG1334          77 LGELVVKIIDKDTGEVIRQIPPEEALELAARMRDVIGILF  116 (120)
T ss_pred             CCCEEEEEEECCCCCCHHHCCHHHHHHHHHHHHHHHHHEE
T ss_conf             5947999997888711021882999999999998661200


No 25 
>TIGR01472 gmd GDP-mannose 4,6-dehydratase; InterPro: IPR006368   This family represent GDP-mannose 4,6-dehydratase, also known as GDP-D-mannose dehydratase. This enzyme converts GDP-mannose to GDP-4-dehydro-6-deoxy-D-mannose, the first of three steps for the conversion of GDP-mannose to GDP-fucose in animals, plants, and bacteria. In bacteria, GDP-L-fucose acts as a precursor of surface antigens such as the extracellular polysaccharide colanic acid of Escherichia coli. Excluded from this family are members of the clade that are poorly related because of highly dervied (phylogenetically long-branch) sequences, e.g. Aneurinibacillus thermoaerophilus Gmd, described as a bifunctional GDP-mannose 4,6-dehydratase/GDP-6-deoxy-D-lyxo-4-hexulose reductase .; GO: 0008446 GDP-mannose 46-dehydratase activity, 0019673 GDP-mannose metabolic process, 0005622 intracellular.
Probab=28.74  E-value=26  Score=16.90  Aligned_cols=107  Identities=20%  Similarity=0.245  Sum_probs=59.1

Q ss_pred             HHHHHHHHHCCCCEEE------EEEECC--CEEEEECHHHHHHHHHHHHHCCCCCCCEEEECCCCCCCCCCCCEEEEEEE
Q ss_conf             9999999861531145------798479--59999868989999999871878980147513256887777857999996
Q gi|254780854|r    7 DLGDYIVNSFSGSVRF------AVNSVG--ELSLDVDCGDLVSLCSFLRDDPHCCFVNIIDLCGVDFLSRSNRFDVVYHF   78 (202)
Q Consensus         7 ~L~~~L~~~l~~~I~~------~~~~~~--el~i~V~~~~l~~vl~~LKdd~~~~F~~LiDItaVDyp~~~~RFeVvY~L   78 (202)
                      .|.+.|...-|..|-+      +.+.++  +-|..+..-.-+.+|..+|++.-|+-              .++ -=.|+=
T Consensus        71 ~L~~~i~~~kP~EiYNLAAQSHV~VSFe~PeYTa~~~g~GTLrlLEA~r~hni~gl--------------~~~-~rFYQA  135 (365)
T TIGR01472        71 NLVKLIDEIKPTEIYNLAAQSHVKVSFEIPEYTADVDGIGTLRLLEAVRSHNILGL--------------IKE-IRFYQA  135 (365)
T ss_pred             HHHHHHHHCCCCEEECCCCCCCEEEECCCCCCHHCHHHHHHHHHHHHHHHHHHHCC--------------CCC-EEEEEC
T ss_conf             99999740488634202023710354165200001244317789998742334141--------------203-025524


Q ss_pred             EECCCCCEEEEEEEECCCCEE-E-------CCCCCEECCCCEECCCHHHC---CCEECCCCCCCC
Q ss_conf             615752059982120578501-0-------12233025531011210113---827356798767
Q gi|254780854|r   79 LSPKYNRRLRVKIAVAEGKSV-P-------SIVGIYPGADWFEREVWDMY---GIFFEGHPDLRR  132 (202)
Q Consensus        79 lS~~~n~ri~Vk~~v~e~~~v-p-------Si~~i~p~A~W~ERE~~Dmf---GI~F~gHPdlRR  132 (202)
                      .|-+. ---.-.++=.|.+|. |       =+.--|-..|+  ||+|-||   ||.| ||--.||
T Consensus       136 StSEl-YG~v~~~PQ~E~TPF~PRSPYAaAK~yA~w~tvNY--REAYgL~A~nGILF-NHESP~R  196 (365)
T TIGR01472       136 STSEL-YGEVQEIPQNETTPFYPRSPYAAAKLYAYWITVNY--REAYGLFAVNGILF-NHESPRR  196 (365)
T ss_pred             CCHHH-CCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHEEEE--ECCCCCCHHCCEEE-CCCCCCC
T ss_conf             52311-36555788888887688876899988454310212--10034100035210-4678877


No 26 
>PRK05592 rplO 50S ribosomal protein L15; Reviewed
Probab=28.30  E-value=18  Score=17.82  Aligned_cols=38  Identities=32%  Similarity=0.618  Sum_probs=28.0

Q ss_pred             CCCCCC--CCCCCCCCCCCCEEEEECHHHCEEECCCCEEEEHHHCCC
Q ss_conf             998987--871133778984478876211513126642202221276
Q gi|254780854|r  136 DYGFEG--HPLRKDFPVTGFVELHYDDKVKKVVYRPVELMQEHRDYD  180 (202)
Q Consensus       136 d~~feG--hPLRKDFPltG~~evryd~~~k~v~~epv~l~q~~r~f~  180 (202)
                      ..||||  -||-+=.|--||.      ...++.|++|+|.+= ..|+
T Consensus        47 ~~gFEGGQ~PL~rRlPKrGF~------n~~~~~~~~inL~~L-~~~~   86 (144)
T PRK05592         47 RPGFEGGQMPLYRRLPKRGFT------NIFRKEYAVVNLSDL-AKFE   86 (144)
T ss_pred             CCCCCCCCCCCEEECCCCCCC------CCCCCEEEEECHHHH-HCCC
T ss_conf             987437986427844643666------656534689839998-4366


No 27 
>pfam09860 DUF2087 Uncharacterized protein conserved in bacteria (DUF2087). This domain, found in various hypothetical prokaryotic proteins and transcriptional activators, has no known function.
Probab=26.29  E-value=3.3  Score=22.30  Aligned_cols=35  Identities=43%  Similarity=0.665  Sum_probs=30.9

Q ss_pred             CEECCCCEECCCHHHCCCEECCCCCCCCCCCCCCC
Q ss_conf             30255310112101138273567987677889989
Q gi|254780854|r  105 IYPGADWFEREVWDMYGIFFEGHPDLRRILTDYGF  139 (202)
Q Consensus       105 i~p~A~W~ERE~~DmfGI~F~gHPdlRRiL~d~~f  139 (202)
                      +=|+...-|+|+-+...=.|.+|.-|||-|-|+||
T Consensus        24 f~~g~~ysE~EvN~iL~~~~~D~a~LRR~LVd~g~   58 (71)
T pfam09860        24 FEPGREYSEKEVNAILKRFHEDYALLRRELVDYGF   58 (71)
T ss_pred             CCCCCCCCHHHHHHHHHHHCCCHHHHHHHHHHCCC
T ss_conf             89999649999999999984889999999997786


No 28 
>TIGR02374 nitri_red_nirB nitrite reductase [NAD(P)H], large subunit; InterPro: IPR012744    This entry describes NirB, the large subunit of nitrite reductase [NAD(P)H] (the assimilatory nitrite reductase), which associates with NirD, the small subunit (IPR012748 from INTERPRO). In a few bacteria such as Klebsiella pneumoniae and in fungi, the two regions are fused.; GO: 0008942 nitrite reductase [NAD(P)H] activity, 0050660 FAD binding, 0050661 NADP binding, 0042128 nitrate assimilation.
Probab=23.55  E-value=11  Score=19.14  Aligned_cols=31  Identities=29%  Similarity=0.519  Sum_probs=22.0

Q ss_pred             HHHCCCEECCCCCCCCCCCCCCCC-CCCCCCC
Q ss_conf             011382735679876778899898-7871133
Q gi|254780854|r  117 WDMYGIFFEGHPDLRRILTDYGFE-GHPLRKD  147 (202)
Q Consensus       117 ~DmfGI~F~gHPdlRRiL~d~~fe-GhPLRKD  147 (202)
                      -|||||.-+.-|.+.|=|-+-+|+ ||--||-
T Consensus       615 l~L~G~k~~dLP~~w~~L~~~~~e~G~aY~kA  646 (813)
T TIGR02374       615 LDLFGAKKDDLPKIWKDLVMPGYESGHAYGKA  646 (813)
T ss_pred             EEEECCCHHHHHHHHHHHCCCCCCCHHHHHHH
T ss_conf             00024876431588997405565550778877


No 29 
>pfam09234 DUF1963 Domain of unknown function (DUF1963). This domain is found in a set of hypothetical bacterial proteins. Its exact function has not, as yet, been described.
Probab=23.24  E-value=64  Score=14.49  Aligned_cols=15  Identities=20%  Similarity=0.168  Sum_probs=10.1

Q ss_pred             CCCCCCCEEEEEEEE
Q ss_conf             877778579999966
Q gi|254780854|r   65 FLSRSNRFDVVYHFL   79 (202)
Q Consensus        65 yp~~~~RFeVvY~Ll   79 (202)
                      -|+....|.|+|+=-
T Consensus        62 ~~~~~~~~rV~y~~~   76 (221)
T pfam09234        62 SPEDQTGFRVIYFED   76 (221)
T ss_pred             CCCCCCCCEEEEECC
T ss_conf             834488748999867


No 30 
>PRK04290 30S ribosomal protein S6e; Validated
Probab=21.06  E-value=62  Score=14.55  Aligned_cols=20  Identities=25%  Similarity=0.381  Sum_probs=14.5

Q ss_pred             CCCCCCCCCCCCCCCCCEEE
Q ss_conf             98987871133778984478
Q gi|254780854|r  137 YGFEGHPLRKDFPVTGFVEL  156 (202)
Q Consensus       137 ~~feGhPLRKDFPltG~~ev  156 (202)
                      -+-.|+|||+|-+-++-+.+
T Consensus        56 sDk~GfPMr~~v~g~~r~~l   75 (115)
T PRK04290         56 SDKDGFPMRPDVPGPVRKRI   75 (115)
T ss_pred             CCCCCCCCCCCCCCCCEEEE
T ss_conf             58889712688658756999


No 31 
>pfam02485 Branch Core-2/I-Branching enzyme. This is a family of two different beta-1,6-N-acetylglucosaminyltransferase enzymes, I-branching enzyme and core-2 branching enzyme . I-branching enzyme is responsible for the production of the blood group I-antigen during embryonic development. Core-2 branching enzyme forms crucial side-chain branches in O-glycans.
Probab=20.56  E-value=72  Score=14.15  Aligned_cols=28  Identities=21%  Similarity=0.197  Sum_probs=17.9

Q ss_pred             HHHHHHHHHCCCCCCCEEEECCCCCCCCCC
Q ss_conf             999999871878980147513256887777
Q gi|254780854|r   40 VSLCSFLRDDPHCCFVNIIDLCGVDFLSRS   69 (202)
Q Consensus        40 ~~vl~~LKdd~~~~F~~LiDItaVDyp~~~   69 (202)
                      .-+...|+.+.  ..++.+-|+|-|+|=+.
T Consensus        77 ~~l~~al~~~~--~w~~fi~Ls~~d~Pl~t  104 (242)
T pfam02485        77 RLLANALLLDP--SWDYFVLLSESDIPLKT  104 (242)
T ss_pred             HHHHHHHHCCC--CCCEEEECCCCCCCCCC
T ss_conf             99999983698--77889980577412478


No 32 
>pfam06283 ThuA Trehalose utilisation. This family consists of several bacterial ThuA like proteins. ThuA appears to be involved in utilisation of trehalose. The thuA and thuB genes form part of the trehalose/sucrose transport operon thuEFGKAB, which is located on the pSymB megaplasmid. The thuA and thuB genes are induced in vitro by trehalose but not by sucrose and the extent of its induction depends on the concentration of trehalose available in the medium.
Probab=20.20  E-value=34  Score=16.14  Aligned_cols=106  Identities=16%  Similarity=0.131  Sum_probs=55.2

Q ss_pred             HHHHHHHCCCCCCCEEEECCCCCCCCCCCCEEEEEEEEE----CCCCCEEEEEEEECCCCE---EECCCCCEECCCCEEC
Q ss_conf             999987187898014751325688777785799999661----575205998212057850---1012233025531011
Q gi|254780854|r   42 LCSFLRDDPHCCFVNIIDLCGVDFLSRSNRFDVVYHFLS----PKYNRRLRVKIAVAEGKS---VPSIVGIYPGADWFER  114 (202)
Q Consensus        42 vl~~LKdd~~~~F~~LiDItaVDyp~~~~RFeVvY~LlS----~~~n~ri~Vk~~v~e~~~---vpSi~~i~p~A~W~ER  114 (202)
                      +...|+++..+..+...|..... +++-++|+||-.+..    +...++-.+.-.+...--   +-+.++-++.-.||. 
T Consensus        22 ~~~~l~~~~~f~v~~t~d~~~~~-~~~L~~yDvvv~~~t~g~~~~~~q~~a~~~~v~~GgG~vg~H~a~~~~~~w~~y~-   99 (216)
T pfam06283        22 IAALLEESGGFEVDTTEDPEHLT-DENLAQYDVLVFNGTTGDELSDEQEAALEKYVAEGGGLVGLHSATDAFRNWPEYN-   99 (216)
T ss_pred             HHHHHHHCCCEEEEEECCHHHCC-HHHHHHCCEEEEECCCCCCCCHHHHHHHHHHHHCCCCEEEECCCCCCCCCCHHHH-
T ss_conf             99988555985999974858819-7768538999997899987999999999999985998798565434677888999-


Q ss_pred             CCHHHCCCEECCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             21011382735679876778899898787113377898
Q gi|254780854|r  115 EVWDMYGIFFEGHPDLRRILTDYGFEGHPLRKDFPVTG  152 (202)
Q Consensus       115 E~~DmfGI~F~gHPdlRRiL~d~~feGhPLRKDFPltG  152 (202)
                         +|.|-.|.+||.--.+-..---..||.-+.+|-+.
T Consensus       100 ---~liGg~f~~Hp~~~~~~v~v~d~~HPi~~gl~~~~  134 (216)
T pfam06283       100 ---RLMGGSFKWHPAGEPFTVWVVDPDHPITKGLPESF  134 (216)
T ss_pred             ---HHHCCEECCCCCCCEEEEEECCCCCHHHHCCCCCC
T ss_conf             ---98586032579994699997289995560776567


No 33 
>COG2125 RPS6A Ribosomal protein S6E (S10) [Translation, ribosomal structure and biogenesis]
Probab=20.18  E-value=66  Score=14.39  Aligned_cols=19  Identities=32%  Similarity=0.564  Sum_probs=13.2

Q ss_pred             CCCCCCCCCCCCCCCCEEE
Q ss_conf             8987871133778984478
Q gi|254780854|r  138 GFEGHPLRKDFPVTGFVEL  156 (202)
Q Consensus       138 ~feGhPLRKDFPltG~~ev  156 (202)
                      +-+|+|||.|-|..+-+.+
T Consensus        58 D~~GfPMr~dv~g~~r~ri   76 (120)
T COG2125          58 DKDGFPMRPDVPGPRRVRI   76 (120)
T ss_pred             CCCCCCCCCCCCCCCEEEE
T ss_conf             8888712689878614899


No 34 
>KOG0105 consensus
Probab=20.03  E-value=43  Score=15.54  Aligned_cols=30  Identities=27%  Similarity=0.596  Sum_probs=15.9

Q ss_pred             CCCCEECCCCEE-----CCCHH---------HCCC-EECCCCCCC
Q ss_conf             223302553101-----12101---------1382-735679876
Q gi|254780854|r  102 IVGIYPGADWFE-----REVWD---------MYGI-FFEGHPDLR  131 (202)
Q Consensus       102 i~~i~p~A~W~E-----RE~~D---------mfGI-~F~gHPdlR  131 (202)
                      |+.+=|++.|..     ||+=|         -.|| .|..|.||.
T Consensus       120 VsGLp~SgSWQDLKDHmReaGdvCfadv~rDg~GvV~~~r~eDMk  164 (241)
T KOG0105         120 VSGLPPSGSWQDLKDHMREAGDVCFADVQRDGVGVVEYLRKEDMK  164 (241)
T ss_pred             EECCCCCCCHHHHHHHHHHHCCEEEEEEECCCCEEEEEEEHHHHH
T ss_conf             734899875678899888617712334220662056552056589


Done!